Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Sequence Analysis”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

Sequence-based analysis of the Vitis vinifera L. cv Cabernet Sauvignon grape must mycobiome in three South African vineyards employing distinct agronomic systems

Recent microbiomic research of agricultural habitats has highlighted tremendous microbial biodiversity associated with such ecosystems. In addition, data generated in vineyards have furthermore highlighted significant regional differences in vineyard biodiversity, hinting at the possibility that such differences might be responsible for regional differences in wine style and character, a hypothesis referred to as "microbial terroir." The current study further contributes to this body of work by comparing the mycobiome associated with South African (SA) Cabernet Sauvignon grapes in three neighboring vineyards that employ different agronomic approaches, and comparing the outcome with similar data sets from Californian vineyards. The aim of this study was to fully characterize the mycobiomes associated with the grapes from these vineyards. The data revealed approximately 10 times more fungal diversity than what is typically retrieved from culture-based studies. The Biodynamic vineyard was found to harbor a more diverse fungal community (H = 2.6) than the conventional (H = 2.1) and integrated (H = 1.8) vineyards. The data show that ascomycota are the most abundant phylum in the three vineyards, with Aureobasidium pullulans and its close relative Kabatiella microsticta being the most dominant fungi. This is the first report to reveal a high incidence of K. microsticta in the grape/wine ecosystem. Different common wine yeast species, such as Metschnikowia pulcherrima and Starmerella bacillaris dominated the mycobiome in the three vineyards. The data show that the filamentous fungi are the most abundant community in grape must although they are not regarded as relevant during wine fermentation. Comparison of metagenomic datasets from the three SA vineyards and previously published data from Californian vineyards revealed only 25% of the fungi in the SA dataset was also present in the Californian dataset, with greater variation evident amongst ubiquitous epiphytic fungi.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Biogeochemical controls on iron speciation and cycling across upland to shoreline gradients in freshwater and estuarine coastal soils (Lake Erie and Chesapeake Bay, United States)

Coastal environments are dynamic interfaces that mediate carbon and nutrient exchanges between terrestrial landscapes and open waters, and understanding the biogeochemical factors controlling these exchanges, particularly iron (Fe) redox transformations, is crucial for predicting coastal ecosystem functions. Here, we investigated the mechanisms controlling Fe speciation changes across upland-to-shoreline gradients in freshwater and estuarine soils using Fe K-edge X-ray absorption spectroscopy, solid and porewater composition analysis, and 16S rRNA sequencing analysis. We show that Fe transformations depend primarily on inundation patterns. In unsaturated uplands, Fe occurs as Fe(III) oxyhydroxides, mainly goethite (9–35 %), Fe(II,III)-phyllosilicates (39–89 %), and Fe(III)-organic species (0–61 %). Soils influenced by estuarine waters exhibit porewater sulfide concentrations reaching up to 221 μM, Fe- and S-cycling bacteria, and up to 81 % pyrite (FeS 2 ), indicating that sulfur-driven redox dynamics control Fe transformations. In lacustrine wetlands, Fe(III) reduction is indicated by porewater Fe(II) concentrations increasing to 1.0–2.1 mM, and ~10–15 % of Fe as Fe(II,III)-(hydr)oxides (green rust), vivianite (Fe 3 (PO 4 ) 2 ·8H 2 O), and/or adsorbed Fe(II) species. EXAFS data also indicate reduction of structural Fe(III) to Fe(II) in phyllosilicates. The presence of Fe- and S-cycling bacteria, as well as sulfide (0–10 μM), suggests that Fe-cycling is microbially driven and potentially coupled with cryptic S-cycling. Fe(II) oxidation was indicated above/near the water table by the presence of Fe(III) oxyhydroxides (ferrihydrite, lepidocrocite). Furthermore, negligible Fe(III) or sulfate reduction was observed at some water-saturated sites located at the upland-wetland transition, likely due to oxic (sub-)surface water inputs. Overall, our results highlight the importance of considering both Fe-speciation and hydro-biogeochemical dynamics when predicting Fe-cycling at coastal interfaces.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Barcoded reciprocal hemizygosity analysis via sequencing illuminates the complex genetic basis of yeast thermotolerance

Decades of successes in statistical genetics have revealed the molecular underpinnings of traits as they vary across individuals of a given species. But standard methods in the field cannot be applied to divergences between reproductively isolated taxa. Genome-wide reciprocal hemizygosity mapping (RH-seq), a mutagenesis screen in an interspecies hybrid background, holds promise as a method to accelerate the progress of interspecies genetics research. Here, we describe an improvement to RH-seq in which mutants harbor barcodes for cheap and straightforward sequencing after selection in a condition of interest. As a proof of concept for the new tool, we carried out genetic dissection of the difference in thermotolerance between two reproductively isolated budding yeast species. Experimental screening identified dozens of candidate loci at which variation between the species contributed to the thermotolerance trait. Hits were enriched for mitosis genes and other housekeeping factors, and among them were multiple loci with robust sequence signatures of positive selection. Together, these results shed new light on the mechanisms by which evolution solved the problems of cell survival and division at high temperature in the yeast clade, and they illustrate the power of the barcoded RH-seq approach.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1986

Mission analysis flow sequencing optimization

This investigation is an extension of a project dealing with the problem of optimal use of ground resources for future space missions. This problem was formulated as a linear programming problem using an indirect approach. Instead of minimizing the inventory level of needed ground resources, the overlapping periods during which the same types of resources are used by various flights are minimized. The model was built upon the assumption that during the time interval under consideration, the costs of various needed resources remain constant. Under other assumptions concerning costs of resources, the objective function, in general, assumes a non-linear form. In this study, one case where the form of the objective function turns out to be quadratic is considered. Also, disadvantages and limitations of the approach used are briefly discussed.

Scott, M.↗
NASA NTRS1990

Analysis of sequencing and scheduling methods for arrival traffic

The air traffic control subsystem that performs scheduling is discussed. The function of the scheduling algorithms is to plan automatically the most efficient landing order and to assign optimally spaced landing times to all arrivals. Several important scheduling algorithms are described and the statistical performance of the scheduling algorithms is examined. Scheduling brings order to an arrival sequence for aircraft. First-come-first-served scheduling (FCFS) establishes a fair order, based on estimated times of arrival, and determines proper separations. Because of the randomness of the traffic, gaps will remain in the scheduled sequence of aircraft. These gaps are filled, or partially filled, by time-advancing the leading aircraft after a gap while still preserving the FCFS order. Tightly scheduled groups of aircraft remain with a mix of heavy and large aircraft. Separation requirements differ for different types of aircraft trailing each other. Advantage is taken of this fact through mild reordering of the traffic, thus shortening the groups and reducing average delays. Actual delays for different samples with the same statistical parameters vary widely, especially for heavy traffic.

Neuman, Frank↗
DOE OSTI2013

Structure-sequence based analysis for identification of conserved regions in proteins

Disclosed are computational methods, and associated hardware and software products for scoring conservation in a protein structure based on a computationally identified family or cluster of protein structures. A method of computationally identifying a family or cluster of protein structures in also disclosed herein.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Comprehensive Detection of Genes Causing a Phenotype Using Phenotype Sequencing and Pathway Analysis

Discovering all the genetic causes of a phenotype is an important goal in functional genomics. We combine an experimental design for detecting independent genetic causes of a phenotype with a high-throughput sequencing analysis that maximizes sensitivity for comprehensively identifying them. Testing this approach on a set of 24 mutant strains generated for a metabolic phenotype with many known genetic causes, we show that this pathway-based phenotype sequencing analysis greatly improves sensitivity of detection compared with previous methods, and reveals a wide range of pathways that can cause this phenotype. We demonstrate our approach on a metabolic re-engineering phenotype, the PEP/OAA metabolic node in E. coli, which is crucial to a substantial number of metabolic pathways and under renewed interest for biofuel research. Out of 2157 mutations in these strains, pathway-phenoseq discriminated just five gene groups (12 genes) as statistically significant causes of the phenotype. Experimentally, these five gene groups, and the next two high-scoring pathway-phenoseq groups, either have a clear connection to the PEP metabolite level or offer an alternative path of producing oxaloacetate (OAA), and thus clearly explain the phenotype. These high-scoring gene groups also show strong evidence of positive selection pressure, compared with strictly neutral selection in the rest of the genome.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1972

An interdisciplinary analysis of ERTS data for Colorado mountain environments using ADP Techniques

Author identified significant preliminary results from the Ouachita portion of the Texoma frame of data indicate many potentials in the analysis and interpretation of ERTS data. It is believed that one of the more significant aspects of this analysis sequence has been the investigation of a technique to relate ERTS analysis and surface observation analysis. At present a sequence involving (1) preliminary analysis based solely upon the spectral characteristics of the data, followed by (2) a surface observation mission to obtain visual information and oblique photography to particular points of interest in the test site area, appears to provide an extremely efficient technique for obtaining particularly meaningful surface observation data. Following such a procedure permits concentration on particular points of interest in the entire ERTS frame and thereby makes the surface observation data obtained to be particularly significant and meaningful. The analysis of the Texoma frame has also been significant from the standpoint of demonstrating a fast turn around analysis capability. Additionally, the analysis has shown the potential accuracy and degree of complexity of features that can be identified and mapped using ERTS data.

Hoffer, R. M.↗
NASA NTRS1972

A study of the utilization of ERTS-A data from the Wabash River Basin

The author has identified the following significant results. Preliminary results from the Texoma frame of data indicate many potentials in the analysis and interpretation of ERTS-1 data. It is believed that one of the more significant aspects of this analysis sequence has been the investigation of a technique to relate ERTS analysis and surface observation analysis. At present a sequence involving (1) preliminary analysis based solely upon the spectral characteristics of the data, followed by (2) a surface observation mission to obtain visual information and oblique color photography of particular points of interest in the test site area, appears to provide an extremely efficient technique for obtaining particularly meaningful surface observation data. Following such a procedure allows concentration on particular points of interest in the entire ERTS frame and thereby making the surface observation data obtained to be particularly significant and meaningful. The analysis of the Texoma frame has also been significant from the standpoint of demonstrating a fast turn around analysis capability. Additionally, the analysis has shown the potential accuracy and degree of complexity of features that can be identified and mapped using ERTS-1 data.

Landgrebe, D. A.↗
DOE OSTI2016

Next generation sequencing data of a defined microbial mock community

Generating sequence data of a defined community composed of organisms with complete reference genomes is indispensable for the benchmarking of new genome sequence analysis methods, including assembly and binning tools. Moreover the validation of new sequencing library protocols and platforms to assess critical components such as sequencing errors and biases relies on such datasets. We here report the next generation metagenomic sequence data of a defined mock community (Mock Bacteria ARchaea Community; MBARC-26), composed of 23 bacterial and 3 archaeal strains with finished genomes. These strains span 10 phyla and 14 classes, a range of GC contents, genome sizes, repeat content and encompass a diverse abundance profile. Short read Illumina and long-read PacBio SMRT sequences of this mock community are described. These data represent a valuable resource for the scientific community, enabling extensive benchmarking and comparative evaluation of bioinformatics tools without the need to simulate data. As such, these data can aid in improving our current sequence data analysis toolkit and spur interest in the development of new tools.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1972

Land utilization and water resource inventories over extended test sites

In addition to the work on the corn blight this year, several other analysis tests were completed which resulted in significant findings. These aspects are discussed as follows: (1) field spectral measurements of soil conditions; (2) analysis of extended test site data; this discussion involves three different sets of data analysis sequences; (3) urban land use analysis, for studying water runoff potentials; and (4) thermal data quality study, as an expansion of our water resources studies involving temperature calibration techniques.

Hoffer, R. M.↗
DOE OSTI2017

Atractiella rhizophila , sp. nov., an endorrhizal fungus isolated from the Populus root microbiome

We discovered a new endorrhizal fungal species belonging to the rust lineage Pucciniomycotina among fungi isolated from healthy root mycobiomes of Populus and described here as Atractiella rhizophila. Here, we characterized this species by transmission electron microscopy (TEM), phylogenetic analysis, and plant bioassay experiments. Phylogenetic sequence analysis of isolates and available environmental and reference sequences indicates that this new species, A. rhizophila, has a broad geographic and host range. Atractiella rhizophila appears to be present in North America, Australia, Asia, and Africa and is associated with trees, orchids, and other agriculturally important species, including soybean, corn, and rice. Despite the large geographic and host range of this species sampling, A. rhizophila appears to have exceptionally low sequence variation within nuclear rDNA markers examined. With inoculation studies, we show that A. rhizophila is nonpathogenic, asymptomatically colonizes plant roots, and appears to foster plant growth and elevated photosynthesis rates.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1987

Phylogenetic diversity and position of the genus Campylobacter

RNA sequence analysis has been used to examine the phylogenetic position and structure of the genus Campylobacter. A complete 5S rRNA sequence was determined for two strains of Campylobacter jejuni and extensive partial sequences of the 16S rRNA were obtained for several strains of C. jejuni and Wolinella succinogenes. In addition limited partial sequence data were obtained from the 16S rRNAs of isolates of C. coli, C. laridis, C. fetus, C. fecalis, and C. pyloridis. It was found that W. succinogenes is specifically related to, but not included, in the genus Campylobacter as presently constituted. Within the genus significant diversity was noted. C. jejuni, C. coli and C. laridis are very closely related but the other species are distinctly different from one another. C. pyloridis is without question the most divergent of the Campylobacter isolates examined here and is sufficiently distinct to warrant inclusion in a separate genus. In terms of overall position in bacterial phylogeny, the Campylobacter/Wolinella cluster represents a deep branching most probably located within an expanded version of the Division containing the purple photosynthetic bacteria and their relatives. The Campylobacter/Wolinella cluster is not specifically includable in either the alpha, beta or gamma subdivisions of the purple bacteria.

NASA Discipline Exobiology↗
NASA NTRS1993

Assignment of fatty acid-beta-oxidizing syntrophic bacteria to Syntrophomonadaceae fam. nov. on the basis of 16S rRNA sequence analyses

After enrichment from Chinese rural anaerobic digestor sludge, anaerobic, sporing and nonsporing, saturated fatty acid-beta-oxidizing syntrophic bacteria were isolated as cocultures with H2- and formate-utilizing Methanospirillum hungatei or Desulfovibrio sp. strain G-11. The syntrophs degraded C4 to C8 saturated fatty acids, including isobutyrate and 2-methylbutyrate. They were adapted to grow on crotonate and were isolated as pure cultures. The crotonate-grown pure cultures alone did not grow on butyrate in either the presence or the absence of some common electron acceptors. However, when they were reconstituted with M. hungatei, growth on butyrate again occurred. In contrast, crotonate-grown Clostridium kluyveri and Clostridium sticklandii, as well as Clostridium sporogenes, failed to grow on butyrate when these organisms were cocultured with M. hungatei. The crotonate-grown pure subcultures of the syntrophs described above were subjected to 16S rRNA sequence analysis. Several previously documented fatty acid-beta-oxidizing syntrophs grown in pure cultures with crotonate were also subjected to comparative sequence analyses. The sequence analyses revealed that the new sporing and nonsporing isolates and other syntrophs that we sequenced, which had either gram-negative or gram-positive cell wall ultrastructure, all belonged to the phylogenetically gram-positive phylum. They were not closely related to any of the previously known subdivisions in the gram-positive phylum with which they were compared, but were closely related to each other, forming a new subdivision in the phylum. We recommend that this group be designated Syntrophomonadaceae fam. nov.; a description is given.

NASA Discipline Number 52-30↗
DOE OSTI2019

Distributed hydrological, chemical, and microbiological measurements around Meander A of East River, Colorado.

In July-August 2018, we collected 88 filtered pore water samples at 20 cm depth and analyzed them for anions, cations, dissolved organic carbon, dissolved organic matter (DOM) quality, and standard water quality parameters. Vertical hydraulic head gradients were measured to assess the potential for upward or downward water flow and sediment grab samples were taken for grain size analyses to constrain the relationship between streambed morphology and water flow. Lastly, DNA was extracted from pore water filters for a 16S rRNA gene sequencing analysis. This allowed for a high-resolution characterization of streambed hydrology and biogeochemistry during base flow. Data.csv includes coordinates, time of sampling, grain size analysis D10 values, vertical hydraulic head gradients, microbiological diversity metrics, and multiple chemical analyses. ReadMe.txt contains all information regarding sampling procedure, analysis instrumentation, and reporting limits. Microbiological sequences analyzed here have been deposited in the NCBI Sequence Read Archive and may be accessed using accession number PRJNA527829.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Optimizing Cell-based Antimicrobials through Pooled Genomic Libraries

DNA synthesis and assembly technologies ushered in through synthetic biology have great promise for biomanufacturing, bioremediation, and the development of living therapeutics. Unfortunately, predicting sequence to function relationships, including for biosynthetic pathways expressed in a new host organism, is difficult and often requires many iterative cycles of design, construction, and testing. We are working to develop data-driven approaches to identify the genetic determinants of growth defects and productivity for the expression of a cell-based antimicrobial. We assayed the growth, pigment production, and antimicrobial activity of a collection of over 10,000 genetic mutants of the violacein biosynthetic pathway and sequenced the genetic variation of these mutants. Through this project, we have developed an innovative codebase to automate the determination of pigmentation and antimicrobial clearing diameter for tens of thousands of genetic mutants cultivated on agar dishes. Further, we have written DNA sequence analysis code to demultiplex & provide consensus sequences from high-throughput PacBio long-read circular consensus sequencing (CCS) datasets. From this foundation, we plan to map DNA sequence to function to predict an optimal genetic design to maximize antimicrobial activity while minimizing deleterious growth effects. The workflows and algorithms developed through this project can be broadly applied to other engineered functions in microbes, uncovering sequence to function relationships for complex phenotypes where function impacts fitness.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2002

Genes encoding calmodulin-binding proteins in the Arabidopsis genome

Analysis of the recently completed Arabidopsis genome sequence indicates that approximately 31% of the predicted genes could not be assigned to functional categories, as they do not show any sequence similarity with proteins of known function from other organisms. Calmodulin (CaM), a ubiquitous and multifunctional Ca(2+) sensor, interacts with a wide variety of cellular proteins and modulates their activity/function in regulating diverse cellular processes. However, the primary amino acid sequence of the CaM-binding domain in different CaM-binding proteins (CBPs) is not conserved. One way to identify most of the CBPs in the Arabidopsis genome is by protein-protein interaction-based screening of expression libraries with CaM. Here, using a mixture of radiolabeled CaM isoforms from Arabidopsis, we screened several expression libraries prepared from flower meristem, seedlings, or tissues treated with hormones, an elicitor, or a pathogen. Sequence analysis of 77 positive clones that interact with CaM in a Ca(2+)-dependent manner revealed 20 CBPs, including 14 previously unknown CBPs. In addition, by searching the Arabidopsis genome sequence with the newly identified and known plant or animal CBPs, we identified a total of 27 CBPs. Among these, 16 CBPs are represented by families with 2-20 members in each family. Gene expression analysis revealed that CBPs and CBP paralogs are expressed differentially. Our data suggest that Arabidopsis has a large number of CBPs including several plant-specific ones. Although CaM is highly conserved between plants and animals, only a few CBPs are common to both plants and animals. Analysis of Arabidopsis CBPs revealed the presence of a variety of interesting domains. Our analyses identified several hypothetical proteins in the Arabidopsis genome as CaM targets, suggesting their involvement in Ca(2+)-mediated signaling networks.

NASA Discipline Plant Biology↗
NASA NTRS1999

A novel beta-glucosidase from the cell wall of maize (Zea mays L.): rapid purification and partial characterization

Plants have a variety of glycosidic conjugates of hormones, defense compounds, and other molecules that are hydrolyzed by beta-glucosidases (beta-D-glucoside glucohydrolases, E.C. 3.2.1.21). Workers have reported several beta-glucosidases from maize (Zea mays L.; Poaceae), but have localized them mostly by indirect means. We have purified and partly characterized a 58-Ku beta-glucosidase from maize, which we conclude from a partial sequence analysis, from kinetic data, and from its localization is not identical to any of those already reported. A monoclonal antibody, mWP 19, binds this enzyme, and localizes it in the cell walls of maize coleoptiles. An earlier report showed that mWP19 inhibits peroxidase activity in crude cell wall extracts and can immunoprecipitate peroxidase activity from these extracts, yet purified preparations of the 58 Ku protein had little or no peroxidase activity. The level of sequence similarity between beta-glucosidases and peroxidases makes it unlikely that these enzymes share epitopes in common. Contrary to a previous conclusion, these results suggest that the enzyme recognized by mWP19 is not a peroxidase, but there is a wall peroxidase closely associated with the 58 Ku beta-glucosidase in crude preparations. Other workers also have co-purified distinct proteins with beta-glucosidases. We found no significant charge in the level of immunodetectable beta-glucosidase in mesocotyls or coleoptiles that precedes the red light-induced changes in the growth rate of these tissues.

Non-NASA Center↗